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9r3c

;Recombinant human butyrylcholinesterase in complex with N-([(3S)-1-benzylpiperidin-3-yl]methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide ;

Method: X-RAY DIFFRACTION D_max: 76.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r3c
deposition_date	2025-05-03
title	;Recombinant human butyrylcholinesterase in complex with N-([(3S)-1-benzylpiperidin-3-yl]methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide ;
keywords	Butyrylcholinesterase, inhibitor, complex, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	24.36 Å
rg_electron	23.06 Å
i0	62432900.00
molecular_weight	62905.0 kDa
excluded_volume	79114 Å³
envelope_volume	90486 Å³
shell_volume	31316 Å³
envelope_diameter	78.7 Å
shell_rg	31.55 Å
envelope_rg	23.46 Å
shape_rg	22.99 Å
total_rg	24.19 Å
total_atoms	4435
n_residues	527
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	76.7 Å
rg_real	24.20 Å
rg_real_error	0.37 Å
i0_real	6.2430e+07
i0_real_error	7.7490e+05
rg_reciprocal	24.24 Å
i0_reciprocal	62430000.0000
total_estimate	0.8938
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.4 Å
skewness	0.169
kurtosis	-0.412
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	19980000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.958

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Cholinesterase
formula_weight	59713.5 kDa
ec_number	3.1.1.8
mutation	;N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide) ;
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4576

EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	man
entity_count	3

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	2

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	N-{[(3S)-1-benzylpiperidin-3-yl]methyl}-N-(2-methoxyethyl)naphthalene-2-sulfonamide
formula_weight	452.6 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	99

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6. Citations (1)

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length_a	154.864 Å
length_b	154.864 Å
length_c	127.326 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 4 2 2
int_tables_number	97
crystal_system	tetragonal

resolution	2.310 Å
resolution_low	49.180 Å
r_factor	0.1919
r_work	0.1900
r_free	0.2293

fit	/app/data/saxs_computation/r3/9r3c/9r3c.fit
pddf	/app/data/pr_computation/r3/9r3c/9r3c.pr.out
profile	/app/data/saxs_computation/r3/9r3c/9r3c.dat